Assignment brief
Collagen IV (ColIV) is an essential component of the basement membrane, and the genes encoding this protein are evolutionarily conserved within the Animal Kingdom (this will be explained more in lectures). Regarding this protein, you are requested to carry out the following two tasks and write a 1500 ± 10% word dissertation summarising the results of your analysis.
A. Identifythecandidatetranscriptionfactorsthatareinvolvedintheexpressionofthe ColIV genes.
For three of the identified genes, review what is known about them. For example, you can summarise their functions, where and when in the body they are expressed, their homology to other known genes, etc.
The strategy to carry out the tasks is as follows:
As the model, you will use the ColIV genes of the fruit fly Drosophila melanogaster. In the Drosophila embryo, the majority of ColIV is produced by cells called haemocytes, which are the equivalent of macrophages in the fly. The DNA sequence that regulates the expression of the ColIV genes has been identified (more details will be explained in lectures).
Exploiting this knowledge, the candidate genes will be identified as follows (Detailed methods will be explained in lectures):
- From the GEO database (https://www.ncbi.nlm.nih.gov/geo/), obtain the list of the genes expressed in haemocytes.
- Using the JASPAR database (https://jaspar.genereg.net/), list the transcription factors that may bind to the regulatory sequence of the ColIV genes.
- For the two lists of the genes obtained above, draw a Venn diagram and identify the genes included in the intersection of the two circles.
Subsequently, from the genes identified, pick any three and review what is known about them (e.g., functions, expression patterns, and homology to other genes). The selection of the three can be either based on your interest or at random. The information about the chosen genes should be researched using Flybase (http://flybase.org/) and PubMed (https://pubmed.ncbi.nlm.nih.gov). How to use these databases will be explained in lectures. Write brief reviews of the information found. The format of the dissertation is instructed in the submission format section below.
Submission format
Please write a 1500 (±10 %) word dissertation that should be structured as follows:
1. Background – Briefly explain the structure of the ColIV genes, using the information provided in lectures.
- Methods – Explain how you found the genes of interest.
- Results – Prepare the lists of the genes found in 1) GEO, 2) JASPAR, and 3) both databases. Put the full list of the genes in tables at the end of the dissertation. Select three genes from the list, and review what is known about them (max 150 words per gene).
- Discussion – explain what you think is interesting about the genes you identified. Some speculation is OK, but try to support your statement by data as much as possible. For example, you may write “this gene is highly expressed in haemocytes thus it is likely to be functioning in them” or “a mutant of this gene shows phenotype X (cite a reference); this may be caused by an abnormality of the basement membrane”.
- Include at least one illustration drawn by yourself. This could be e.g., the structure of the ColIV genes, the conservation of the structure, or the key Venn diagram. It does not need to be too artistic (though you can be so if you want); simple cartoons made by PowerPoint objects are enough and often the best.
- You are encouraged to use figures, especially those made by yourself. If you copy/modify figures from published literature, you must indicate the source.
- Your dissertation must have a logical, clear, and scientifically credible structure. Your references should mainly come from peer-reviewed journal articles, but you can also use less formal sources such as textbooks and official websites showing statistical data (e.g., those from World Health Organisation, National Health Service, etc.).
- Cite references in your text with the (Author Year) format, and provide the full reference list in the Harvard format after discussion.
- The reference list, plus figures, tables and their captions do not count towards the word count.
Marking criteria
Key areas assessed will be:
- 1) The factual and conceptual understanding of the subject matter. (12%)
- 2) The evidence of wider reading which goes beyond unit material. (12%)
- 3) The level of analysis and evaluation of information. (12%)
- 4) The structure and clarity of the work. (6%)
